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@jcnamendiOdysseus
jcnamendiOdysseus committed Dec 29, 2023
1 parent 1fa1d69 commit b9b5820
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Showing 16 changed files with 228 additions and 107 deletions.
45 changes: 22 additions & 23 deletions src/main/java/org/ohdsi/circe/check/checkers/Comparisons.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,7 @@

import java.time.LocalDate;
import java.time.format.DateTimeParseException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.*;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import org.apache.commons.lang3.builder.EqualsBuilder;
Expand All @@ -31,6 +29,12 @@

public class Comparisons {

private static final Map<String, Integer> TIME_UNIT_CONVERSION = new HashMap<>();
static {
TIME_UNIT_CONVERSION.put(IntervalUnit.HOUR.getName(), 60 * 60);
TIME_UNIT_CONVERSION.put(IntervalUnit.MINUTE.getName(), 60);
}

public static Boolean startIsGreaterThanEnd(NumericRange r) {

return Objects.nonNull(r.value) && Objects.nonNull(r.extent) && r.value.intValue() > r.extent.intValue();
Expand Down Expand Up @@ -101,31 +105,26 @@ public static Predicate<Concept> compare(Concept source) {
.append(concept.vocabularyId, source.vocabularyId)
.build();
}

public static int compareTo(ObservationFilter filter, Window window) {
int range1 = (filter.postDays + filter.priorDays) * 24 * 60 * 60;
int range2Start = getTimeInSeconds(window.start);
int range2End = getTimeInSeconds(window.end);
int range1 , range2Start , range2End;
if(Objects.nonNull(window.start) && Objects.nonNull(window.start.days)){
range1 = filter.postDays + filter.priorDays;
range2Start = window.start.coeff * window.start.days;
range2End = Objects.nonNull(window.end) && Objects.nonNull(window.end.days) ? window.end.coeff * window.end.days : 0;
}else {
range1 = (filter.postDays + filter.priorDays) * 24 * 60 * 60;
range2Start = getTimeInSeconds(window.start);
range2End = getTimeInSeconds(window.end);
}
return range1 - (range2End - range2Start);
}

private static int getTimeInSeconds(Window.Endpoint endpoint) {
if (Objects.isNull(endpoint)) {
return 0;
return Optional.ofNullable(endpoint)
.map(ep -> {
int convertRate = TIME_UNIT_CONVERSION.getOrDefault(ep.timeUnit, 1);
return Objects.nonNull(ep.timeUnitValue) ? ep.coeff * ep.timeUnitValue * convertRate : 0;
}).orElse(0);
}
int convertRate;
if (endpoint.timeUnit.equals(IntervalUnit.DAY.getName())) {
convertRate = 24 * 60 * 60;
} else if (endpoint.timeUnit.equals(IntervalUnit.HOUR.getName())) {
convertRate = 60 * 60;
} else if (endpoint.timeUnit.equals(IntervalUnit.MINUTE.getName())) {
convertRate = 60;
} else convertRate = 1;
return Objects.nonNull(endpoint.timeUnitValue)
? endpoint.coeff * endpoint.timeUnitValue * convertRate
: 0;
}


public static boolean compare(Criteria c1, Criteria c2) {

Expand Down
25 changes: 17 additions & 8 deletions src/main/java/org/ohdsi/circe/check/checkers/ExitCriteriaDaysOffsetCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,14 +18,17 @@

package org.ohdsi.circe.check.checkers;

import static org.ohdsi.circe.check.operations.Operations.match;
import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;

import java.util.Objects;
import org.ohdsi.circe.check.WarningSeverity;
import org.ohdsi.circe.cohortdefinition.CohortExpression;
import org.ohdsi.circe.cohortdefinition.DateOffsetStrategy;

import java.util.Arrays;
import java.util.List;
import java.util.Objects;

import static org.ohdsi.circe.check.operations.Operations.match;
import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;

public class ExitCriteriaDaysOffsetCheck extends BaseCheck {

private static final String DAYS_OFFSET_WARNING = "Cohort Exit criteria: %ss offset from start date should be greater than 0";
Expand All @@ -40,9 +43,15 @@ protected WarningSeverity defineSeverity() {
protected void check(CohortExpression expression, WarningReporter reporter) {

match(expression.endStrategy)
.isA(DateOffsetStrategy.class)
.then(s -> match((DateOffsetStrategy)s)
.when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) && 0 == dateOffsetStrategy.offsetUnitValue)
.then(dateOffsetStrategy -> reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit))));
.isA(DateOffsetStrategy.class)
.then(s -> match((DateOffsetStrategy)s)
.when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) && (0 == dateOffsetStrategy.offset || 0 == dateOffsetStrategy.offsetUnitValue))
.then(dateOffsetStrategy -> {
if(0 == dateOffsetStrategy.offset){
reporter.add(String.format(DAYS_OFFSET_WARNING), "Days");
}else {
reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit));
}
}));
}
}
7 changes: 5 additions & 2 deletions src/main/java/org/ohdsi/circe/check/checkers/FirstTimeInHistoryCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,11 @@ protected void checkCriteria(CorelatedCriteria criteria, String groupName, Warni
Execution addWarning = () -> reporter.add(WARNING, name);
match(criteria)
.when(c -> c.startWindow != null && ((c.startWindow.start != null
&& c.startWindow.start.timeUnitValue != null) || (c.startWindow.end != null
&& c.startWindow.end.timeUnitValue != null)))
&& c.startWindow.start.days != null) || (c.startWindow.end != null
&& c.startWindow.end.days != null))
|| ((c.startWindow.start.timeUnitValue != null)
&& (c.startWindow.end != null)
&& c.startWindow.end.timeUnitValue != null))
.then(cc -> match(cc.criteria)
.isA(ConditionEra.class)
.then(c -> match((ConditionEra)c)
Expand Down
26 changes: 18 additions & 8 deletions src/main/java/org/ohdsi/circe/check/checkers/RangeCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
import org.ohdsi.circe.cohortdefinition.Window;

import java.util.Objects;
import java.util.Optional;

public class RangeCheck extends BaseValueCheck {
private static final String NEGATIVE_VALUE_ERROR = "Time window in criteria \"%s\" has negative value %d at %s";
Expand Down Expand Up @@ -52,15 +53,24 @@ protected void checkInclusionRules(final CohortExpression expression, WarningRep
}

private void checkWindow(Window window, WarningReporter reporter, String name) {
Optional.ofNullable(window)
.map(w -> checkEndpoint(w, name, "start"))
.ifPresent(reporter::add);

if (Objects.nonNull(window)) {
if (Objects.nonNull(window.start) && Objects.nonNull(window.start.timeUnitValue) && window.start.timeUnitValue < 0) {
reporter.add(NEGATIVE_VALUE_ERROR, name, window.start.timeUnitValue, "start");
}
if (Objects.nonNull(window.end) && Objects.nonNull(window.end.timeUnitValue) && window.end.timeUnitValue < 0) {
reporter.add(NEGATIVE_VALUE_ERROR, name, window.end.timeUnitValue, "end");
}
}
Optional.ofNullable(window)
.map(w -> checkEndpoint(w, name, "end"))
.ifPresent(reporter::add);
}

private String checkEndpoint(Window window, String name, String endpointType) {
boolean hasValid = Objects.nonNull(window.start) && Objects.nonNull(window.start.days < 0 ? window.start.days : window.start.timeUnitValue) && window.start.days < 0 ? window.start.days < 0 : window.start.timeUnitValue < 0;
return Optional.of(window)
.filter(w -> hasValid)
.map(w -> String.format(NEGATIVE_VALUE_ERROR, name, getEndpointValue(w.start), endpointType))
.orElse(null);
}
private Object getEndpointValue(Window.Endpoint endpoint) {
return Objects.nonNull(endpoint.days) ? endpoint.days : endpoint.timeUnitValue;
}

private void checkObservationFilter(ObservationFilter filter, WarningReporter reporter, String name) {
Expand Down
25 changes: 17 additions & 8 deletions src/main/java/org/ohdsi/circe/check/checkers/TimePatternCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,7 @@

package org.ohdsi.circe.check.checkers;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import org.ohdsi.circe.check.WarningSeverity;
Expand Down Expand Up @@ -83,17 +80,29 @@ private String formatTimeWindow(TimeWindowInfo ti) {
}

private String formatDays(Window.Endpoint endpoint) {
return Objects.nonNull(endpoint.timeUnitValue) ? String.valueOf(endpoint.timeUnitValue) : "all";
return Objects.nonNull(endpoint.days) ? String.valueOf(endpoint.days) :
Objects.nonNull(endpoint.timeUnitValue) ? String.valueOf(endpoint.timeUnitValue) : "all";

}

private String formatCoeff(Window.Endpoint endpoint) {
return endpoint.coeff < 0 ? "before " : "after ";
}


private Integer startDays(Window window) {
return Objects.nonNull(window) && Objects.nonNull(window.start) ?
(Objects.nonNull(window.start.timeUnitValue) ? window.start.timeUnitValue : 0) * window.start.coeff : 0;
}
return Optional.ofNullable(window)
.map(w -> w.start)
.map(start -> {
int coefficient = Optional.ofNullable(start.coeff).orElse(0);
return Optional.ofNullable(start.days)
.map(days -> days * coefficient)
.orElseGet(() -> Optional.ofNullable(start.timeUnitValue)
.map(timeUnitValue -> timeUnitValue * coefficient)
.orElse(0));
})
.orElse(0);
}

class TimeWindowInfo {
private String name;
Expand Down
58 changes: 36 additions & 22 deletions src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,8 @@

import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import org.apache.commons.lang3.StringUtils;
Expand Down Expand Up @@ -351,10 +350,12 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ

resultSql = StringUtils.replace(resultSql, "@cohort_end_unions", StringUtils.join(endDateSelects, "\nUNION ALL\n"));

// resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
resultSql = StringUtils.replace(resultSql, "@era_pad", Integer.toString(expression.collapseSettings.eraPadUnitValue));

if(!StringUtils.isEmpty(Integer.toString(expression.collapseSettings.eraPad)) && expression.collapseSettings.eraPad != 0){
resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
}else{
resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
resultSql = StringUtils.replace(resultSql, "@era_pad", Integer.toString(expression.collapseSettings.eraPadUnitValue));
}
resultSql = StringUtils.replace(resultSql, "@inclusionRuleTable", getInclusionRuleTableSql(expression));
resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByEventQuery", getInclusionAnalysisQuery("#qualified_events", 0));
resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByPersonQuery", getInclusionAnalysisQuery("#best_events", 1));
Expand Down Expand Up @@ -548,20 +549,25 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
Window startWindow = criteria.startWindow;
String startIndexDateExpression = (startWindow.useIndexEnd != null && startWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
String startEventDateExpression = (startWindow.useEventEnd != null && startWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
if (startWindow.start.timeUnitValue != null) {
startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
if (startWindow.start.days != null) {
startExpression = String.format("DATEADD(day,%d,%s)", startWindow.start.coeff * startWindow.start.days, startIndexDateExpression);
} else if (startWindow.start.timeUnitValue != null) {
startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
} else {
startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
}

if (startExpression != null) {
clauses.add(String.format("%s >= %s", startEventDateExpression, startExpression));
}

if (startWindow.end.timeUnitValue != null) {
endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
if (startWindow.end.days != null) {
endExpression = String.format("DATEADD(day,%d,%s)", startWindow.end.coeff * startWindow.end.days, startIndexDateExpression);
}
else if (startWindow.end.timeUnitValue != null) {
endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
} else {
endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
}

if (endExpression != null) {
Expand All @@ -575,20 +581,24 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
String endIndexDateExpression = (endWindow.useIndexEnd != null && endWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
// for backwards compatability, having a null endWindow.useIndexEnd means they SHOULD use the index end date.
String endEventDateExpression = (endWindow.useEventEnd == null || endWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
if (endWindow.start.timeUnitValue != null) {
startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
if (endWindow.start.days != null) {
startExpression = String.format("DATEADD(day,%d,%s)", endWindow.start.coeff * endWindow.start.days, endIndexDateExpression);
} else if (endWindow.start.timeUnitValue != null) {
startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
} else {
startExpression = checkObservationPeriod ? (endWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
startExpression = checkObservationPeriod ? (endWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
}

if (startExpression != null) {
clauses.add(String.format("%s >= %s", endEventDateExpression, startExpression));
}

if (endWindow.end.timeUnitValue != null) {
endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
if (endWindow.end.days != null) {
endExpression = String.format("DATEADD(day,%d,%s)", endWindow.end.coeff * endWindow.end.days, endIndexDateExpression);
} else if (endWindow.end.timeUnitValue != null) {
endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
} else {
endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
}

if (endExpression != null) {
Expand Down Expand Up @@ -765,10 +775,13 @@ private String getDateFieldForOffsetStrategy(DateOffsetStrategy.DateField dateFi
@Override
public String getStrategySql(DateOffsetStrategy strat, String eventTable) {
String strategySql = StringUtils.replace(DATE_OFFSET_STRATEGY_TEMPLATE, "@eventTable", eventTable);
strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
if(strat.offset != 0){
strategySql = StringUtils.replace(strategySql, "@offset", Integer.toString(strat.offset));
}else {
strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
}
strategySql = StringUtils.replace(strategySql, "@dateField", getDateFieldForOffsetStrategy(strat.dateField));

return strategySql;
}

Expand All @@ -793,4 +806,5 @@ public String getStrategySql(CustomEraStrategy strat, String eventTable) {
}

// </editor-fold>

}
4 changes: 3 additions & 1 deletion src/main/java/org/ohdsi/circe/cohortdefinition/CollapseSettings.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,10 @@ public class CollapseSettings {

@JsonProperty("CollapseType")
public CollapseType collapseType = CollapseType.ERA;
@JsonProperty("EraPad")
public int eraPad = 0;
@JsonProperty("EraPadUnit")
public String eraPadUnit = IntervalUnit.DAY.getName();
public String eraPadUnit;
@JsonProperty("EraPadUnitValue")
public int eraPadUnitValue = 0;

Expand Down
5 changes: 3 additions & 2 deletions src/main/java/org/ohdsi/circe/cohortdefinition/DateOffsetStrategy.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,14 +30,15 @@ public enum DateField {
StartDate,
EndDate
}

@JsonProperty("Offset")
public int offset = 0;
@JsonProperty("DateField")
public DateField dateField = DateField.StartDate;

@JsonProperty("OffsetUnitValue")
public int offsetUnitValue = 0;
@JsonProperty("OffsetUnit")
public String offsetUnit = IntervalUnit.DAY.getName();
public String offsetUnit;

@Override
public String accept(IGetEndStrategySqlDispatcher dispatcher, String eventTable) {
Expand Down
1 change: 0 additions & 1 deletion src/main/java/org/ohdsi/circe/cohortdefinition/IntervalUnit.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
import jdk.nashorn.internal.objects.annotations.Getter;

public enum IntervalUnit {
DAY("day"),
HOUR("hour"),
MINUTE("minute"),
SECOND("second");
Expand Down
10 changes: 3 additions & 7 deletions src/main/java/org/ohdsi/circe/cohortdefinition/builders/ConditionOccurrenceSqlBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,9 @@
import org.ohdsi.circe.cohortdefinition.ConditionOccurrence;
import org.ohdsi.circe.helper.ResourceHelper;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.text.SimpleDateFormat;
import java.util.*;

import org.ohdsi.circe.cohortdefinition.DateAdjustment;

import static org.ohdsi.circe.cohortdefinition.builders.BuilderUtils.buildDateRangeClause;
Expand Down Expand Up @@ -65,7 +62,6 @@ protected String embedCodesetClause(String query, T criteria) {

@Override
protected String embedOrdinalExpression(String query, T criteria, List<String> whereClauses) {

// first
if (criteria.first != null && criteria.first == true) {
whereClauses.add("C.ordinal = 1");
Expand Down
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